What is hydrogen breath testing and how does it work?

By September 29, 2016Health

Dr. James Brief

Gastroenterologist, FoodMarble co-founder and Chief Medical Officer

If you have ever looked for solutions to your digestive issues, you may have come across something called “hydrogen breath testing.” What is this test, why is this test done and how does it work?

To answer those questions, I will first need to do a quick review on how the digestive system works. As we all know, when we swallow food it goes into our stomach. There, it soaks in stomach acids for about 30–60 minutes. This is done in an effort to kill most of the bacteria, viruses and parasites in our food.

After the stomach, the food bolus travels into the small intestine.

There, enzymes from the liver and pancreas break nutrients down to their smallest components so they can be absorbed into the bloodstream. This is where we absorb sugars, fats, proteins and vitamins. After that, the food then passes into the large intestine (also called the colon) where water is absorbed. Anything remaining after that is eliminated from the body as waste (poop/feces/solid waste).

One last thing to know is that in every human’s large intestine/colon, we have billions and billions of bacteria. When confined to the colon, these bacteria have many health benefits. Unfortunately, there are other times where these bacteria cause problems for humans.

Earlier I mentioned that sugars are absorbed when the food travels through the small intestine. Therefore, by the time the food enters the large intestine, there isn’t much (if any) sugar left in the remaining food bolus. There are some circumstances, however, where sugars are not absorbed in the small intestine and do enter the large intestine.

In these situations, the bacteria eat the sugars, potentially causing a host of problems.

Bacteria digest sugars in a process called fermentation. In fermentation, sugars are broken down into gases such as hydrogen & methane. When fermentation occurs in the colon, this causes the release of a large amount of gases, causing symptoms such as bloating, abdominal pain and diarrhea. Think of it like a balloon inflating inside your belly (ouch).

The gases created by fermentation are then absorbed into the bloodstream. Eventually, when blood reaches the lungs, these gases are expelled from the body in our breath.

Gases are released in the gut, absorbed into the blood and released on the breath.
Gases are released in the gut, absorbed into the blood and released on the breath.
Fermentation of food into gas in the colon, seeps into the blood, transfers to the lungs and exits on the breath


This is where hydrogen breath testing come in. We can deduce when the bacteria in our intestines are fermenting sugars by looking for these gases in our breath.

Human beings do not produce hydrogen.

Imagine a scenario in which a person fasts for 24 hours, without eating food or water. In this scenario, the person’s digestive system is completely empty. If we were to take a sample of that person’s breath, we would not detect any hydrogen because there are no sugars in the gut for the bacteria to digest.

Now imagine we give this person some sugar and it gets absorbed easily in their small intestine. If they were to provide a breath sample every 15 minutes for 3 hours, their hydrogen levels would stay low. Why is that? Since the sugar given to them is absorbed easily, none of it enters the large intestine (where the bacteria live) and no fermentation would have taken place:

When food isn't fermenting in the gut, hydrogen levels remain low.
Example of a “negative” hydrogen breath test


Now let’s take the example of a person who does not digest sugars well. You have probably heard of the term “lactose intolerance.” This is a disorder in which a sugar called lactose is poorly digested in a person’s small intestine. In this scenario, lactose travels undigested into the large intestine. Once there, it is fermented by the bacteria which release hydrogen and methane into the gut, causing pain, bloating and diarrhea.

Let’s imagine this lactose intolerant person eats a big bowl of vanilla ice cream. If a breath sample were to be taken from this person every 15 minutes for 3 hours, the graph will look quite different than the one before. This time, we would be able to detect the gases created by the bacteria in the gut:

When food is fermenting in the gut, hydrogen level rise over time.
Example of a “positive” hydrogen breath test suggestive of bacterial fermentation


I’ll break this down so that you can understand what the graph is telling us. Remember that human beings do not produce hydrogen. Therefore, if we see a rise in hydrogen after eating food, we can attribute this rise to bacterial fermentation in the gut. Let’s take another look at that last hydrogen breath reading, this time with some notes added in:

The stages of a hydrogen increase during a hydrogen breath test.
Breakdown of a “positive” hydrogen breath test


As you can see, the dramatic rise in hydrogen about an hour after eating signifies bacterial fermentation in the gut. Once these products of fermentation dissolve into the bloodstream and travel to the lungs, they can be detected by a hydrogen/methane breath analyzer. This is how doctors diagnose their patients with lactose intolerance, fructose intolerance and a number of other disorders.

Small Intestinal Bacterial Overgrowth

In addition to detecting food intolerances, breath testing has also been used to detect bacterial infections in the gut. In particular, some gastroenterologists use breath testing to diagnose a disorder called SIBO (Small Intestinal Bacterial Overgrowth). There has been some controversy over using breath testing to diagnose SIBO and this is the topic I will discuss in my next blog entry.

I hope I have made breath testing a little more clear for you. Please leave me any comments, feedback or questions you may have regarding breath testing or any other digestive problems you may be experiencing. I’d love to hear from you!